Contacts of the strand formed by residues 307 - 315 (chain B) in PDB entry 3OCH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202B ILE* 3.2 15.5 - - + +
204B LEU* 3.7 22.4 - - + -
303B PHE 3.2 9.5 + - - +
304B LEU* 3.0 20.5 + - + +
306B LYS* 1.3 78.6 - - - +
308B GLN* 1.3 62.0 + - - +
309B LYS 4.3 9.2 - - - +
310B LEU* 4.6 2.7 - - + -
333B TRP* 3.8 1.0 - - - -
358B ARG* 2.9 29.3 + - - -
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Residues in contact with GLN 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B MET* 3.9 26.0 - - + +
202B ILE 2.9 7.2 + - - +
305B PRO 5.5 1.2 + - - -
306B LYS 3.9 7.5 + - - +
307B ALA* 1.3 76.0 + - - +
309B LYS* 1.3 60.0 + - - +
333B TRP* 3.6 6.7 - - - -
357B GLU* 3.5 5.2 - - - +
358B ARG* 2.9 73.1 + - - +
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B MET* 4.3 20.7 - - + +
202B ILE 3.8 1.7 + - - +
203B SER* 3.2 14.8 - - - +
204B LEU 2.9 23.2 + - - -
290B GLU* 3.7 5.8 - - - +
307B ALA* 3.6 2.2 - - - +
308B GLN* 1.3 81.4 - - - +
310B LEU* 1.3 70.1 + - - +
311B TYR* 3.4 39.2 + - + +
333B TRP* 3.8 0.6 - - - -
336B VAL* 5.7 0.6 - - - +
355B ILE* 4.0 15.8 - - + +
356B LEU 3.2 11.9 - - - +
357B GLU* 3.8 30.0 + - - -
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 3.4 24.9 - - + -
304B LEU* 3.9 20.9 - - + -
307B ALA* 4.6 2.0 - - + -
309B LYS* 1.3 86.3 - - - +
311B TYR* 1.3 62.3 + - - +
312B LEU* 3.8 21.4 + - + -
325B PHE* 4.3 9.9 - - + -
328B TYR* 4.4 15.5 - - + -
333B TRP* 3.6 37.7 - - + -
354B GLU 3.7 0.5 - - - +
355B ILE* 3.3 4.2 - - - +
356B LEU* 2.8 53.0 + - + +
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Residues in contact with TYR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B SER* 3.6 11.0 - - - -
204B LEU 2.7 18.6 + - - -
205B ILE* 3.3 17.6 - - + +
206B ALA 3.0 25.5 + - - +
230B TRP* 4.1 7.8 + + + +
234B ASN* 3.4 39.3 - - + -
238B LYS* 3.6 5.4 + - - -
290B GLU* 2.6 36.5 + - - -
292B MET* 3.6 16.6 - - + -
309B LYS* 3.4 27.8 + - + +
310B LEU* 1.3 76.7 - - - +
312B LEU* 1.3 60.3 + - - +
354B GLU 3.3 7.0 - - - +
355B ILE* 3.7 26.7 - - + +
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204B LEU 5.1 1.3 - - - +
206B ALA* 3.4 7.4 - - + +
208B LEU* 4.1 21.5 - - + -
230B TRP* 5.0 2.0 + - - -
310B LEU* 4.0 14.8 - - + +
311B TYR* 1.3 81.8 - - - +
313B THR* 1.3 61.3 + - - +
314B HIS* 3.8 24.6 + - + +
325B PHE* 3.9 25.6 - - + -
328B TYR* 3.4 34.3 - - + +
352B CYS 3.4 2.3 - - - +
353B PHE* 3.7 0.9 - - - -
354B GLU* 2.8 39.3 + - + +
356B LEU* 3.8 18.2 - - + -
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Residues in contact with THR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A 2MX 3.5 6.8 + - - -
206B ALA 2.9 13.1 + - - -
207B ALA* 3.5 3.4 - - - -
208B LEU 2.8 30.5 + - - +
227B ASP* 2.7 32.1 + - + +
230B TRP* 3.5 6.2 + - - -
312B LEU* 1.3 72.1 - - - +
314B HIS* 1.3 60.1 + - - +
315B ILE* 3.6 10.6 + - + +
351B TYR* 3.8 24.2 - - + -
352B CYS 3.4 3.4 - - - +
353B PHE* 3.4 30.0 - - + +
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Residues in contact with HIS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B LEU* 3.7 19.3 - - + +
312B LEU* 4.0 31.7 - - + +
313B THR* 1.3 71.8 - - - +
315B ILE* 1.3 60.7 + - - +
316B ASP 4.2 0.3 + - - -
328B TYR* 4.3 9.0 - - - -
340B PHE* 5.9 0.3 - - - -
350B SER 4.0 0.3 - - - +
351B TYR* 3.2 2.9 - - - -
352B CYS* 2.9 57.0 + - + +
354B GLU* 3.0 34.4 + - + -
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Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B ALA* 3.7 18.8 - - + -
208B LEU 2.9 11.2 + - - +
209B ALA* 3.5 13.3 - - - -
210B VAL* 3.6 6.2 + - - +
222B TRP* 3.4 49.1 - - + -
224B LEU* 3.3 28.5 - - + -
227B ASP* 5.1 0.4 - - - -
313B THR* 3.8 20.0 - - + +
314B HIS* 1.3 77.3 - - - +
316B ASP* 1.3 60.0 + - - +
317B ALA* 2.9 11.5 + - + -
349B HIS* 3.7 17.7 - - + -
350B SER 3.4 11.4 - - - +
351B TYR* 4.2 4.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il